ArticleNucleic acids research2023
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
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Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it, 82 citations in OpenAlex.
- Computational prediction of RNA modification site-disease associations: a systematic review.Briefings in bioinformatics · 2026Pooled it
- RNA modifications as determinants of cancer cell death: from epitranscriptomic mechanisms to therapeutic targeting.Functional & integrative genomics · 2026Review
- Ion chromatography-ultra-high-resolution mass spectrometry reveals EZH2-driven reprogramming of nucleic acid and protein methylation.Analytica chimica acta · 2026Article
- DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.Genomics, proteomics & bioinformatics · 2026Article
- VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Mke-resnet: a lightweight and interpretable deep learning framework for efficient RNA m6A site identification.BMC bioinformatics · 2026Article
- RMzyme: regulations of RNA-modifying enzymes in humans.Signal transduction and targeted therapy · 2026Article
- Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.Nature communications · 2026Article
- RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- m6AConquer: a consistently quantified and orthogonally validated database for the N6-methyladenosine (m6A) epitranscriptome.Nucleic acids research · 2026Article
- Functional Prediction of Epitranscriptome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Multiomics Approaches for Bacteriophage-Based Biocontrol Applications: A Review of Metabolomics, Transcriptomics, and Proteomics.BioMed research international · 2026Review
- m6AHD: a new framework for identifying abnormal N6-methyladenosine (m6A) in heart diseases based on sequencing features.Frontiers in genetics · 2026Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A robust deep learning framework for RNA 5-methyluridine modification prediction using integrated features.BMC biology · 2025Article
- DirectRM: integrated detection of landscape and crosstalk between multiple RNA modifications using direct RNA sequencing.Nature communications · 2025Article
- YModPred: an interpretable prediction method for multi-type RNA modification sites in S. cerevisiae based on deep learning.BMC biology · 2025Article
- Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With advanced technologies to map RNA modifications, our understanding of them has been revolutionized, and they are seen to be far more widespread and important than previously thought. Current next-generation sequencing (NGS)-based modification profiling methods are blind to RNA modifications and thus require selective chemical treatment or antibody immunoprecipitation methods for particular modification types. They also face the problem of short read length, isoform ambiguities, biases and artifacts. Direct RNA sequencing (DRS) technologies, commercialized by Oxford Nanopore Technologies (ONT), enable the direct interrogation of any given modification present in individual transcripts and promise to address the limitations of previous NGS-based methods. Here, we present the first ONT-based database of quantitative RNA modification profiles, DirectRMDB, which includes 16 types of modification and a total of 904,712 modification sites in 25 species identified from 39 independent studies. In addition to standard functions adopted by existing databases, such as gene annotations and post-transcriptional association analysis, we provide a fresh view of RNA modifications, which enables exploration of the epitranscriptome in an isoform-specific manner. The DirectRMDB database is freely available at: http://www.rnamd.org/directRMDB/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.